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AMD in Action: Fighting Infectious Disease on Many Fronts

During the fall of 2014, a multi-state outbreak of listeriosis sent 34 people to the hospital; seven people died. Listeriosis is caused by the germ Listeria. Listeriosis is rare, but it strikes hard at the most vulnerable people – older adults, pregnant women, newborn babies, and people with weakened immune systems. Because listeriosis can be deadly, it is important to identify the source of the germ quickly to keep more people from getting sick. However, Listeria is difficult to identify and can lurk in foods that we don’t suspect.

While doing routine virus isolation from a blood sample collected from a patient enrolled in a study of Heartland virus, a recently discovered tick-associated virus, CDC microbiologist Olga Kosoy’s keen eye saw something unexpected: evidence of another virus. Because it seemed completely different, she asked CDC scientist Amy Lambert to sequence the virus genome using the powerful tools of Advanced Molecular Detection (AMD). Both were surprised to find that they had discovered an entirely new human pathogen.

In mid-August 2014, hospitals in Missouri and Illinois notified CDC of an increase in admissions of children with severe respiratory illness. The hospitals sent specimens to CDC’s Polio and Picornavirus Laboratory to sequence the virus and determine the type. CDC identified enterovirus D68 (EV-D68) in most of the specimens.

With the largest Ebola outbreak in history raging through West Africa, understanding whether the virus is changing as it spreads through different populations can help responders know what treatments to use and also help research laboratories develop new tools to speed diagnosis in the field.

The diagnosis of a drug-resistant “nightmare bacteria” in two Colorado patients spurred hospital and state health officials to join forces with CDC to investigate. These bacteria — Carpabenem-resistant Enterobacteriaceae, or CRE — have become resistant to all or nearly all of the antibiotics we have today. Untreatable and hard-to-treat infections from CRE germs are on the rise among patients in medical facilities.

Scientists traced a hepatitis A outbreak affecting 162 people to a berry blend product. Whole genome sequencing and advanced analytic methods helped them identify a shipment of pomegranate seeds from Turkey as the source of the outbreak.

In routine food testing, the Canadian Food Inspection Agency found Listeria in bagged lettuce. Investigators conducted whole genome sequencing and found one of the closest matches between an infected person and a contaminated food product that they had ever seen.

When polio broke out in the Horn of Africa in 2013, Kenya lab technicians quickly identified the source as a wild virus and sent specimens to CDC. Overnight, CDC scientists sequenced the virus and identified it as coming from Nigeria—on the other side of the continent.